As the pitch approaches the 10nm node, in order to meet current and future patterning challenges, high resolution techniques are required, complementary to extreme ultraviolet lithography (EUVL) for high volume manufacturing of nanodevices. These complementary techniques should have the following specifications: 1) High patterning resolution, below 10 nm; 2) capability of patterning in 3D; 3) sufficient wafer-scale throughput; 4) the capability of closed loop metrology and 5) the capability of measuring nondestructively through layers, for alignment and overlay applications.<p> </p> Scanning probe microscopy (SPM) has shown a great degree of nano-scale control, and a great potential to address the challenges found in metrology. There has been a broad development of SPM-based methods for patterning and metrology purposes although its exploitation for technological applications is limited due to the modest throughput of scanning probe based techniques. In this article we present experimental results that include the proof-of-principle of using SSURFM to locate existing buried nanopatterns (lines of 50 nm) and subsequently using our patterning technology to manufacture nanocontact holes aligned to the existing buried lines. In combination with the high throughput parallel scanning probe, this example demonstrates the great potential and the suitability of the group of technologies developed at TNO (consisting of the patterning and the subsurface nanoimaging) for alignment and overlay, especially through opaque layers.